Using Microbes To Convert Heavy Metals
September 30, 2012

Microbial Zoo Found At Contaminated Uranium Mill Could Help Toxic Cleanup

Brett Smith for - Your Universe Online

New research from University of California at Berkeley scientists could have a big impact on toxic metal clean-up at hundreds of sites around the United States and the world.

Using a groundbreaking metagenomic sequencing analysis on underground microbes at a contaminated uranium mill in Colorado, the UC Berkeley research team identified 150,000 genes that were assigned to 80 different microbes that live in the soil, according to their report in the journal Science.

The team said they hope their findings lead to improvements in toxic clean-up technology that use microbes to convert heavy metals, like arsenic and mercury, into inert, harmless chemical forms that pose little risk of contaminating the water supply.

During the analysis of the genetic data, the team was surprised to find out how the massive microbial community at the site was comprised. They expected to find mostly Geobacter bemidjiensis, a well-known metal-reducing bacterium. However, the team also found genetic evidence of bacteria presumably feeding on dead Geobacter and other carbon in the soil. These fermentative microorganisms produce hydrogen and organic compounds as a byproduct of their metabolism.

"What we found was like a microbial zoo," said lead author Kelly C. Wrighton, a UC Berkeley post-doctoral fellow. "We thought that the respiring organisms — those breathing metals and making carbon dioxide — were our heavy lifters, but we found that fermentative organisms probably underpin their metabolism.”

“These organisms produce as a bi-product acetate, lactate and ethanol as well as hydrogen and those are all components that these respiring organisms can use,” she added.

According to the researchers, the metagenomic analysis proves the validity methods developed by Jill Banfield at UC Berkeley. The technique involves the sequencing of a jumble of genes and assigning them to specific microbes, even if there are nearly 100 bacteria in the sample. Before this method was devised, metagenomic analyses were unable to assign genes to specific microbes.

"The techniques developed in Jill's lab for doing metagenomics of very complex microbial communities is giving us a much more accurate look at what the microbes are doing and how we can modify them to get them to do more effectively what we want them to do, which is reduce uranium to form a solid," said Philip E. Long, a geologist at UC Berkeley´s Lawrence Berkeley National Laboratory (LBNL). "We are finding out from these studies that the subsurface microbial economy is different from what we thought."

The team said they hope to continue mining the site for a more comprehensive view of the microbial community that lives there and that people could harness these microbes for conservation and safety purposes.

"Our research has lifted a veil on a large portion of bacterial life and enabled us to probe in great depth and detail these unknown and uncultured bacteria," said Wrighton, who hopes to use this information to raise the microbes in the laboratory. "We now have information, which is encoded in their genomic DNA, pertaining to what they look like, how they make their living in the environment, and the interactions they have with other organisms."